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Water Quality Certifications

Section 401 of the federal Clean Water Act requires state certification for any permit or license issued by a federal agency for an activity that may result in a discharge into waters of the US. Water quality certifications ensure projects comply with state water quality standards and any other water quality requirements under state law.

An applicant is required to submit a Pre-Filing Meeting Request a minimum of 30 days prior to submitting a Water Quality Certification application.  The pre-filing meeting may determine if an application is necessary.  Please review the 401 Certification Guidance document for further details on the process and timeline.

Once a § 401 certification is requested, DEQ must act within a reasonable period of time, which cannot exceed one year. DEQ can waive certification (either expressly or by taking no action), deny certification, grant certification, or grant certification with conditions. If a certification is issued with conditions, they become conditions of the license or permit and are enforceable.

Download the documents below to start the § 401 certification application process:

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The federal Clean Water Act requires a permit to conduct water-related construction activities such as fills for development, water resource projects, and infrastructure development. The US Army Corps of Engineers is responsible for issuing dredge and fill permits in Idaho.

Section 401 Water Quality Certification Requirements for Section 404 Projects

On January 13, 2021, the United States Army Corps of Engineers (ACE) published a final rule in the Federal Register (86 FR 2744) announcing the reissuance of 12 existing nationwide permits (NWPs) and four new NWPs. These 16 NWPs and their associated conditions went into effect on March 15, 2021, and replace the previous versions.

There are 40 existing NWPs that were issued in 2017 that were not reissued or modified by the January 13, 2021, final rule and will remain in effect until the ACE reissues those NWPs or when they expire on March 18, 2022.

The Idaho Department of Environmental Quality (DEQ) has authority to review activities receiving § 404 dredge and fill permits and issue a water quality certification (WQC) decision (§ 401(a)(1) of the Federal Water Pollution Control Act (Clean Water Act), as amended; 33 U.S.C. § 1341(a)(1); and Idaho Code §§ 39-101 et seq. and 39-3601 et seq.).

DEQ issued a final § 401 WQC on March 3, 2017 for the 2017 NWPs, which will continue to apply to the 40 NWPs that were not reissued. DEQ also issued a final § 401 WQC on December 4, 2020, for the 16 new NWPs. Applicants will either be certified under the 2017 WQC, the 2020 WQC, or need to request an individual WQC depending on which NWP covers the project (see table below). Depending on which NWP an applicant’s activity falls under will depend which WQC they will need to follow or apply for an individual WQC.

The following lists summarizes the certification to which the applicant should refer. For NWPs which the activity is partially denied or denied by DEQ, the applicant is required to apply and obtain an individual certification. The 2017 and 2020 Water Quality Certification links provide further instructions on the individual certification application process.

2017 WQC

  • Afterburner/Oxidizer Form
  • 1 Aids to Navigation
  • 2 Structures in Artificial Canals
  • 3 Maintenance
  • 4 Fish and Wildlife Harvesting, Enhancement, and Attraction Devices and Activities
  • 5 Scientific Measurement Devices
  • 6 Survey Activities
  • 7 Outfall Structures and Associated Intake Structures
  • 8 Oil and Gas Structures on the Outer Continental Shelf
  • 9 Structures in Fleeting and Anchorage Areas
  • 10 Mooring Buoys
  • 11 Temporary Recreational Structures
  • 15 U.S. Coast Guard Approved Bridges
  • 18 Minor Discharges
  • 19 Minor Dredging
  • 20 Response Operation for Oil or Hazardous Substances
  • 22 Removal of Vessels
  • 24 Indian Tribe or State Administered Section 404 Program
  • 25 Structural Discharges
  • 27 Aquatic Habitat Restoration, Establishment, and Enhancement Activities
  • 28 Modification of Existing Marinas
  • 30 Moist Soil Management of Wildlife
  • 31 Maintenance of Existing Flood Control Facilities
  • 32 Completed Enforcement Actions
  • 33 Temporary Construction, Access, and Dewatering
  • 34 Cranberry Production Activities
  • 35 Maintenance Dredging of Existing Basins
  • 36 Boat Ramps
  • 37 Emergency Watershed Protection and Rehabilitation
  • 38 Cleanup of Hazardous and Toxic Waste
  • 41 Reshaping Existing Drainage Ditches
  • 45 Repair of Uplands Damaged by Discrete Events
  • 46 Discharges in Ditches
  • 49 Coal Remaining Activities

2020 WQC

  • 48 Commercial Shellfish Mariculture Activities
  • 55 Seaweed Mariculture Activities
  • 56 Finfish Mariculture Activities

May Require an Individual WQC1

  • 12 Oil or Natural Gas Pipeline Activities
  • 13 Bank Stabilization
  • 14 Linear Transportation Projects
  • 16 Return Water From Upland Contained Disposal Areas
  • 17 Hydropower Projects
  • 21 Surface Coal Mining Activities
  • 23 Approved Categorical Exclusions
  • 29 Residential Developments
  • 39 Commercial and Institutional Developments
  • 40 Agricultural Activities
  • 42 Recreational Facilities
  • 43 Stormwater Management Facilities
  • 44 Mining Activities
  • 50 Underground Coal Mining Activities
  • 51 Land-Based Renewable Energy Generation Facilities
  • 52 Water-Based Renewable Energy Generation Pilot Projects
  • 53 Removal of Low-Head Dams
  • 54 Living Shorelines
  • 57 Electric Utility Line and Telecommunications Activities
  • 58 Utility Line Activities for Water and Other Substances

1. The size and scope of a project will determine if it will be covered under the 2020 WQC or require an individual WQC.

The NPDES program requires facilities discharging from a point source (e.g. a pipe or other conveyance) into waters of the US to obtain a discharge permit. An NPDES permit contains limits on what can be discharged and other provisions to ensure that the discharge does not harm water quality or the public’s health.

A §401 certification is required for any federally issued NPDES permit in Idaho, including all NPDES permits issued prior to the State of Idaho assuming primacy for permitting.

The Federal Energy Regulatory Commission (FERC) is responsible for issuing licenses for the construction of new hydropower projects, relicensing existing projects, and overseeing ongoing project operations, including dam safety inspections and environmental monitoring.

Before FERC may license or relicense non-federal hydroelectric dams, a state certification is required. A company that has applied for a FERC license must request a §401 certification from DEQ. DEQ must grant or deny certification within one year of receipt of the request. If the state has not granted or denied the certification within one year of the request, certification is considered waived.

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